I think it's more that in fiction, real science is shown as being "THE END OF US ALL", and often it's psuedo-science or in fantasy outright magic which is shown as being "THE ONLY THING THAT CAN SAVE US"

Best example would be Captain Planet. ALL the villains use real (or extrapolated) technology exclusively to destroy (Reaching it's peak in Dr Blight, who is mad science embodied), the heroes use sparkly magical powers and a mullet-ed genie to save the world.

In fact, of course, science is fundamentally neutral, it simply IS. It's people who are evil or good and choose the ends to which it's used.